genome.fa.s54.2.7.7.80.10.50.1000.19.html

Tandem Repeats Finder Program written by:

Gary Benson
Program in Bioinformatics
Boston University
Version 4.09

Please cite:
G. Benson,
"Tandem repeats finder: a program to analyze DNA sequences"
Nucleic Acid Research(1999)
Vol. 27, No. 2, pp. 573-580.

Sequence: Scaffold54
Parameters: 2 7 7 80 10 50 1000
Length:  3629595

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   

This is table  19  of  20  ( 2342 repeats found )

Click on indices to view alignment

Table Explanation

Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3311569--3311601	17	2.1	16	88	11	50	69	3	0	27	1.03
3311864--3311898	10	3.4	10	88	4	52	34	0	0	65	0.93
3315374--3315419	19	2.3	19	85	7	56	45	2	2	50	1.26
3317248--3317382	13	9.4	14	67	23	59	45	0	0	54	0.99
3317274--3317373	19	5.5	19	73	22	90	45	0	0	55	0.99
3317275--3317356	31	2.5	33	88	7	116	43	0	0	56	0.99
3317340--3317385	19	2.4	19	85	10	58	52	0	0	47	1.00
3317358--3317396	20	1.9	19	85	10	51	53	0	0	46	1.00
3317339--3317396	22	2.8	21	79	7	57	50	0	0	50	1.00
3317356--3317426	38	1.9	38	83	11	94	53	0	0	46	1.00
3317400--3317453	22	2.4	23	81	12	67	61	0	0	38	0.96
3317399--3317448	21	2.3	21	80	12	57	62	0	0	38	0.96
3318582--3318618	3	12.0	3	88	5	56	35	2	0	62	1.10
3318721--3318759	20	2.0	21	85	10	55	66	0	0	33	0.92
3329174--3329211	2	19.0	2	100	0	76	50	0	0	50	1.00
3331040--3331081	21	2.0	20	82	13	50	54	4	0	40	1.21
3331414--3331454	2	20.5	2	100	0	82	51	0	0	48	1.00
3332101--3332136	18	2.0	18	88	0	54	38	2	0	58	1.13
3333109--3333140	2	16.0	2	93	0	55	53	0	0	46	1.00
3335064--3335141	25	3.2	26	80	8	74	60	0	1	38	1.05
3335064--3335164	19	5.2	20	70	14	59	60	0	0	38	1.04
3335064--3335167	38	2.6	40	78	17	110	58	0	0	40	1.04
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3339706--3339739	16	2.1	16	88	0	50	55	5	38	0	1.24
3343169--3343205	2	18.5	2	94	0	65	51	2	0	45	1.15
3343362--3343402	19	2.1	20	86	4	57	60	0	0	39	0.96
3344558--3344614	23	2.5	22	82	5	69	40	0	0	59	0.97
3345176--3345263	25	3.5	25	77	13	83	52	0	0	47	1.00
3349169--3349197	2	14.5	2	100	0	58	51	0	0	48	1.00
3349197--3349227	2	15.5	2	100	0	62	51	0	48	0	1.00
3350094--3350124	2	15.5	2	93	0	53	48	3	0	48	1.17
3353753--3353778	2	13.0	2	100	0	52	0	50	0	50	1.00
3354667--3354693	2	13.5	2	100	0	54	48	0	0	51	1.00
3355333--3356089	248	3.0	250	92	2	1225	42	18	6	32	1.76
3358545--3358683	63	2.2	63	87	1	190	31	14	37	16	1.89
3363035--3363079	21	2.3	19	84	7	54	44	2	4	48	1.35
3363097--3363139	12	3.3	12	83	9	50	34	0	0	65	0.93
3363179--3363221	22	2.0	22	90	4	70	60	0	0	39	0.97
3363827--3363866	21	1.9	21	94	0	71	40	7	5	47	1.54
3364391--3364440	24	2.0	26	92	7	86	46	0	0	54	1.00
3364391--3364429	13	3.2	13	78	14	55	43	0	0	56	0.99
3364393--3364432	11	3.3	12	80	13	55	45	0	0	55	0.99
3364393--3364440	13	3.9	12	78	13	53	45	0	0	54	0.99
3364577--3364619	20	2.0	20	82	8	50	46	4	0	48	1.22
3374616--3374658	16	2.6	17	82	10	54	53	0	0	46	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3375151--3375175	13	1.9	13	100	0	50	68	0	0	32	0.90
3375627--3375652	12	2.2	12	100	0	52	76	0	0	23	0.78
3375695--3375738	16	2.6	17	78	10	54	68	2	0	29	1.02
3375753--3375786	15	2.3	15	90	5	52	64	8	0	26	1.22
3377264--3377310	20	2.4	20	85	3	60	48	0	0	51	1.00
3382914--3383050	63	2.2	64	83	10	167	31	16	33	18	1.93
3386523--3386570	17	2.8	17	83	3	60	50	2	2	45	1.25
3386513--3386579	18	3.7	18	80	6	73	47	1	1	49	1.19
3386627--3386672	23	2.0	23	91	0	74	36	4	0	58	1.18
3386916--3386954	16	2.4	16	82	0	51	84	5	5	5	0.86
3395606--3395670	29	2.3	28	81	5	78	47	0	1	50	1.10
3398310--3398336	2	13.5	2	100	0	54	51	0	48	0	1.00
3403517--3403552	17	2.1	17	100	0	72	36	11	11	41	1.76
3415014--3415047	18	1.9	18	88	5	52	35	5	14	44	1.70
3423152--3423177	2	13.0	2	100	0	52	50	0	0	50	1.00
3430107--3430625	259	2.0	259	96	0	966	32	14	14	38	1.86
3434313--3434350	16	2.4	16	79	16	51	15	5	7	71	1.28
3438850--3438880	2	15.5	2	100	0	62	0	51	0	48	1.00
3443368--3443404	17	2.2	17	86	13	51	70	0	5	24	1.08
3444057--3444123	25	2.6	27	79	18	79	59	2	2	34	1.28
3444596--3444637	17	2.4	18	84	11	52	45	0	2	52	1.13
3444675--3444768	22	4.0	24	75	16	83	60	0	0	39	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3444693--3444770	24	3.3	23	75	22	74	58	0	0	41	0.98
3460601--3460636	2	18.0	2	100	0	72	50	0	50	0	1.00
3463615--3463738	48	2.6	48	97	0	230	30	12	20	36	1.89
3474710--3474789	16	4.8	17	76	19	71	37	0	2	60	1.11
3474702--3474789	18	5.4	16	75	18	67	38	0	2	59	1.10
3477786--3477810	2	12.5	2	100	0	50	48	0	0	52	1.00
3482310--3482399	44	2.0	44	100	0	180	25	26	18	28	1.98
3484821--3484873	21	2.5	21	84	3	61	64	1	0	33	1.05
3485306--3485357	14	3.5	14	76	21	52	36	0	0	63	0.95
3485323--3485445	61	2.1	58	85	13	162	42	0	0	57	0.98
3485650--3485695	15	3.1	15	76	14	51	28	0	0	71	0.86
3486398--3486612	34	6.4	34	81	2	236	27	6	24	40	1.81
3486398--3486612	102	2.1	101	87	1	313	27	6	24	40	1.81
3490917--3491137	34	6.5	33	84	5	271	25	7	25	40	1.82
3490917--3491135	102	2.2	101	89	1	330	26	7	25	40	1.82
3491565--3491598	16	2.1	17	89	10	54	64	0	0	35	0.94
3493359--3493402	22	1.9	24	90	9	74	0	20	0	79	0.73
3493842--3493904	31	2.0	32	84	3	83	53	3	7	34	1.46
3494565--3494606	14	2.9	15	79	13	61	66	0	0	33	0.92
3494697--3494737	19	2.2	19	91	4	66	0	9	4	85	0.73
3496255--3496327	4	19.0	4	80	8	71	4	19	0	76	0.94
3496251--3496327	23	3.3	23	75	12	77	3	18	0	77	0.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3496381--3496436	3	19.0	3	96	3	105	66	0	0	33	0.92
3497679--3497705	13	2.1	13	100	0	54	29	7	40	22	1.81
3500709--3500738	2	15.0	2	92	0	51	53	0	0	46	1.00
3500898--3500939	21	2.0	22	90	4	68	50	0	0	50	1.00
3501700--3501757	23	2.5	24	81	13	68	58	0	0	41	0.98
3502026--3502058	2	16.5	2	100	0	66	48	0	0	51	1.00
3502288--3502325	3	12.7	3	100	0	76	65	0	0	34	0.93
3502896--3502954	13	4.5	13	75	12	50	52	1	0	45	1.10
3503409--3503465	15	4.0	15	73	15	50	35	0	0	64	0.93
3505306--3505334	14	2.1	14	100	0	58	44	13	6	34	1.71
3508024--3508073	21	2.4	21	77	9	59	56	0	2	42	1.11
3508309--3508338	10	3.0	10	95	0	51	73	0	6	20	1.05
3508847--3508903	16	3.6	17	77	11	59	31	1	1	64	1.13
3508851--3508909	28	2.1	29	84	9	77	30	1	1	66	1.12
3509533--3509603	2	39.0	2	72	27	52	53	1	2	42	1.24
3509928--3510047	58	2.0	60	93	3	208	49	0	2	48	1.14
3511946--3512031	7	11.3	7	77	18	50	47	0	0	52	1.00
3511959--3512004	9	5.0	9	82	15	58	45	0	0	54	0.99
3511988--3512030	21	2.0	21	90	9	68	46	0	0	53	1.00
3511982--3512045	27	2.2	30	76	17	73	42	0	0	57	0.98
3519627--3519736	55	2.0	55	98	0	211	31	16	13	38	1.88
3522383--3522420	16	2.5	15	87	8	58	18	18	15	47	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3524946--3524973	3	9.3	3	100	0	56	64	0	0	35	0.94
3532489--3532540	24	2.2	25	83	13	65	57	0	1	40	1.10
3533323--3533355	14	2.4	14	94	0	57	0	9	0	90	0.44
3533647--3533685	2	20.0	2	84	5	53	43	0	0	56	0.99
3533669--3533884	112	1.9	112	96	1	398	37	15	7	39	1.75
3536350--3536404	14	3.8	15	76	21	55	45	1	0	52	1.11
3537173--3537201	2	14.5	2	100	0	58	51	0	0	48	1.00
3537267--3537317	2	24.5	2	92	4	75	50	3	0	45	1.20
3537392--3537419	2	14.0	2	100	0	56	50	0	0	50	1.00
3542325--3542369	23	1.9	24	90	4	74	62	2	0	35	1.08

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20